From eb8d600efc08a5524d78560fb9f2610b67d0c2e3 Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 14 Jan 2025 12:10:26 +0000 Subject: [PATCH] Build branch main with version main (dd1f934) Build pipeline: viash-hub.demultiplex.main-v6krs Source commit: https://github.com/viash-hub/demultiplex/commit/dd1f93487f4e908999504e1fcdf97f6c59f743d9 Source message: Add check for the presence of a 'CopyComplete.txt' file (#34) --- CHANGELOG.md | 7 ++++++ src/demultiplex/config.vsh.yaml | 8 ++++++ src/demultiplex/main.nf | 4 +++ src/runner/config.vsh.yaml | 8 +++++- src/runner/main.nf | 1 + .../interop_summary_to_csv/.config.vsh.yaml | 6 ++--- .../interop_summary_to_csv | 4 +-- target/executable/io/publish/.config.vsh.yaml | 6 ++--- target/executable/io/publish/publish | 4 +-- target/executable/io/untar/.config.vsh.yaml | 6 ++--- target/executable/io/untar/untar | 4 +-- .../dataflow/combine_samples/.config.vsh.yaml | 6 ++--- .../nextflow/dataflow/combine_samples/main.nf | 6 ++--- .../.config.vsh.yaml | 6 ++--- .../gather_fastqs_and_validate/main.nf | 6 ++--- target/nextflow/demultiplex/.config.vsh.yaml | 14 ++++++++--- target/nextflow/demultiplex/main.nf | 21 +++++++++++++--- .../nextflow/demultiplex/nextflow_schema.json | 25 +++++++++++++++++++ .../interop_summary_to_csv/.config.vsh.yaml | 6 ++--- .../io/interop_summary_to_csv/main.nf | 6 ++--- target/nextflow/io/publish/.config.vsh.yaml | 6 ++--- target/nextflow/io/publish/main.nf | 6 ++--- target/nextflow/io/untar/.config.vsh.yaml | 6 ++--- target/nextflow/io/untar/main.nf | 6 ++--- target/nextflow/runner/.config.vsh.yaml | 14 ++++++++--- target/nextflow/runner/main.nf | 18 ++++++++++--- target/nextflow/runner/nextflow_schema.json | 25 +++++++++++++++++++ 27 files changed, 177 insertions(+), 58 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 68ac6c0..387da3e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,10 @@ +# demultiplex v0.3.5 + +## Minor updates + +* In case Illumina data is detected in the input folder, check for the presence of the 'copyComplete.txt' file. + This check can be disabled using `--skip_copycomplete_check` (PR #34). + # demultiplex v0.3.4 ## Minor updates diff --git a/src/demultiplex/config.vsh.yaml b/src/demultiplex/config.vsh.yaml index 07c5916..5351ab4 100644 --- a/src/demultiplex/config.vsh.yaml +++ b/src/demultiplex/config.vsh.yaml @@ -53,6 +53,14 @@ argument_groups: direction: "output" required: true default: "$id/run_information.csv" + - name: "Other arguments" + arguments: + - name: --skip_copycomplete_check + type: boolean_true + description: | + Disable the check for the presence of a "CopyComplete.txt" file in input + directory in case of Illumina data. + resources: - type: nextflow_script path: main.nf diff --git a/src/demultiplex/main.nf b/src/demultiplex/main.nf index 6c10bdc..b593127 100644 --- a/src/demultiplex/main.nf +++ b/src/demultiplex/main.nf @@ -94,6 +94,10 @@ workflow run_wf { // step based on the run dir, not the InterOp dir. def interop_dir = state.input.resolve("InterOp") assert interop_dir.isDirectory(): "Expected InterOp directory to be present." + + def copycomplete_file = state.input.resolve("CopyComplete.txt") + assert (copycomplete_file.isFile() || state.skip_copycomplete_check): + "'CopyComplete.txt' file was not found!" } def resultState = state + newState diff --git a/src/runner/config.vsh.yaml b/src/runner/config.vsh.yaml index 020be85..5359d54 100644 --- a/src/runner/config.vsh.yaml +++ b/src/runner/config.vsh.yaml @@ -49,7 +49,13 @@ argument_groups: type: file direction: output default: "qc/multiqc_report.html" - + - name: "Other arguments" + arguments: + - name: --skip_copycomplete_check + type: boolean_true + description: | + Disable the check for the presence of a "CopyComplete.txt" file in input + directory in case of Illumina data. resources: - type: nextflow_script path: main.nf diff --git a/src/runner/main.nf b/src/runner/main.nf index c705a09..87d21f7 100644 --- a/src/runner/main.nf +++ b/src/runner/main.nf @@ -24,6 +24,7 @@ workflow run_wf { "input": state.input, "run_information": state.run_information, "demultiplexer": state.demultiplexer, + "skip_copycomplete_check": state.skip_copycomplete_check, "output": "fastq", "output_falco": "qc/fastqc", "output_multiqc": "qc/multiqc_report.html", diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml index 88312dc..fe7971b 100644 --- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml @@ -149,9 +149,9 @@ build_info: output: "target/executable/io/interop_summary_to_csv" executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv" viash_version: "0.9.1" - git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983" - git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-15-g8da2bf2" + git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9" + git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-16-gdd1f934" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv index bd7e527..6950f2c 100755 --- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv +++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv @@ -454,9 +454,9 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \ mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv" -LABEL org.opencontainers.image.created="2025-01-14T11:34:29Z" +LABEL org.opencontainers.image.created="2025-01-14T11:56:35Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="8da2bf20c5727df1fcdcc997ae87caf562ac4983" +LABEL org.opencontainers.image.revision="dd1f93487f4e908999504e1fcdf97f6c59f743d9" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml index 12f274f..e907bc2 100644 --- a/target/executable/io/publish/.config.vsh.yaml +++ b/target/executable/io/publish/.config.vsh.yaml @@ -199,9 +199,9 @@ build_info: output: "target/executable/io/publish" executable: "target/executable/io/publish/publish" viash_version: "0.9.1" - git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983" - git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-15-g8da2bf2" + git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9" + git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-16-gdd1f934" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index 902478e..f0adf07 100755 --- a/target/executable/io/publish/publish +++ b/target/executable/io/publish/publish @@ -450,9 +450,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish" -LABEL org.opencontainers.image.created="2025-01-14T11:34:29Z" +LABEL org.opencontainers.image.created="2025-01-14T11:56:35Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="8da2bf20c5727df1fcdcc997ae87caf562ac4983" +LABEL org.opencontainers.image.revision="dd1f93487f4e908999504e1fcdf97f6c59f743d9" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml index 0388586..3ece2f2 100644 --- a/target/executable/io/untar/.config.vsh.yaml +++ b/target/executable/io/untar/.config.vsh.yaml @@ -156,9 +156,9 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.1" - git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983" - git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-15-g8da2bf2" + git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9" + git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-16-gdd1f934" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index 2300f5c..90abcd6 100755 --- a/target/executable/io/untar/untar +++ b/target/executable/io/untar/untar @@ -450,9 +450,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io untar" -LABEL org.opencontainers.image.created="2025-01-14T11:34:29Z" +LABEL org.opencontainers.image.created="2025-01-14T11:56:35Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="8da2bf20c5727df1fcdcc997ae87caf562ac4983" +LABEL org.opencontainers.image.revision="dd1f93487f4e908999504e1fcdf97f6c59f743d9" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml index 0d976b4..c6d7045 100644 --- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml +++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml @@ -147,9 +147,9 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.1" - git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983" - git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-15-g8da2bf2" + git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9" + git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-16-gdd1f934" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index 4c9ce40..4be6dbf 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -3216,9 +3216,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.1", - "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983", - "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-15-g8da2bf2" + "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9", + "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-16-gdd1f934" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml index 7f63365..7150215 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml @@ -141,9 +141,9 @@ build_info: output: "target/nextflow/dataflow/gather_fastqs_and_validate" executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf" viash_version: "0.9.1" - git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983" - git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-15-g8da2bf2" + git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9" + git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-16-gdd1f934" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf index dda64bf..679d838 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf @@ -3209,9 +3209,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.1", - "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983", - "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-15-g8da2bf2" + "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9", + "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-16-gdd1f934" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index 83188aa..da24b4f 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -96,6 +96,14 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" +- name: "Other arguments" + arguments: + - type: "boolean_true" + name: "--skip_copycomplete_check" + description: "Disable the check for the presence of a \"CopyComplete.txt\" file\ + \ in input\ndirectory in case of Illumina data.\n" + info: null + direction: "input" resources: - type: "nextflow_script" path: "main.nf" @@ -239,9 +247,9 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.1" - git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983" - git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-15-g8da2bf2" + git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9" + git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-16-gdd1f934" dependencies: - "target/nextflow/io/untar" - "target/nextflow/dataflow/gather_fastqs_and_validate" diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf index 4155d8e..028d5c0 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -3147,6 +3147,17 @@ meta = [ "multiple_sep" : ";" } ] + }, + { + "name" : "Other arguments", + "arguments" : [ + { + "type" : "boolean_true", + "name" : "--skip_copycomplete_check", + "description" : "Disable the check for the presence of a \\"CopyComplete.txt\\" file in input\ndirectory in case of Illumina data.\n", + "direction" : "input" + } + ] } ], "resources" : [ @@ -3345,9 +3356,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.1", - "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983", - "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-15-g8da2bf2" + "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9", + "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-16-gdd1f934" }, "package_config" : { "name" : "demultiplex", @@ -3495,6 +3506,10 @@ workflow run_wf { // step based on the run dir, not the InterOp dir. def interop_dir = state.input.resolve("InterOp") assert interop_dir.isDirectory(): "Expected InterOp directory to be present." + + def copycomplete_file = state.input.resolve("CopyComplete.txt") + assert (copycomplete_file.isFile() || state.skip_copycomplete_check): + "'CopyComplete.txt' file was not found!" } def resultState = state + newState diff --git a/target/nextflow/demultiplex/nextflow_schema.json b/target/nextflow/demultiplex/nextflow_schema.json index 89ec597..e8bf006 100644 --- a/target/nextflow/demultiplex/nextflow_schema.json +++ b/target/nextflow/demultiplex/nextflow_schema.json @@ -109,6 +109,27 @@ } +} +}, + + + "other arguments" : { + "title": "Other arguments", + "type": "object", + "description": "No description", + "properties": { + + + "skip_copycomplete_check": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete", + "help_text": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete.txt\" file in input\ndirectory in case of Illumina data.\n" + , + "default":false + } + + } }, @@ -153,6 +174,10 @@ "$ref": "#/definitions/output arguments" }, + { + "$ref": "#/definitions/other arguments" + }, + { "$ref": "#/definitions/nextflow input-output arguments" } diff --git a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml index 64234bf..9d1d6a2 100644 --- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml @@ -149,9 +149,9 @@ build_info: output: "target/nextflow/io/interop_summary_to_csv" executable: "target/nextflow/io/interop_summary_to_csv/main.nf" viash_version: "0.9.1" - git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983" - git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-15-g8da2bf2" + git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9" + git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-16-gdd1f934" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf index b339aea..6cd60a8 100644 --- a/target/nextflow/io/interop_summary_to_csv/main.nf +++ b/target/nextflow/io/interop_summary_to_csv/main.nf @@ -3221,9 +3221,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.1", - "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983", - "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-15-g8da2bf2" + "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9", + "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-16-gdd1f934" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index 7c9e2f9..83b9ca6 100644 --- a/target/nextflow/io/publish/.config.vsh.yaml +++ b/target/nextflow/io/publish/.config.vsh.yaml @@ -199,9 +199,9 @@ build_info: output: "target/nextflow/io/publish" executable: "target/nextflow/io/publish/main.nf" viash_version: "0.9.1" - git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983" - git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-15-g8da2bf2" + git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9" + git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-16-gdd1f934" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index d4d1769..f191bb8 100644 --- a/target/nextflow/io/publish/main.nf +++ b/target/nextflow/io/publish/main.nf @@ -3280,9 +3280,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish", "viash_version" : "0.9.1", - "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983", - "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-15-g8da2bf2" + "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9", + "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-16-gdd1f934" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index fc97288..2fab962 100644 --- a/target/nextflow/io/untar/.config.vsh.yaml +++ b/target/nextflow/io/untar/.config.vsh.yaml @@ -156,9 +156,9 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.1" - git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983" - git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-15-g8da2bf2" + git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9" + git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-16-gdd1f934" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index ebbdb43..d9aa6d6 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -3233,9 +3233,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.1", - "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983", - "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-15-g8da2bf2" + "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9", + "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-16-gdd1f934" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml index 6683afb..7a2d161 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -84,6 +84,14 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" +- name: "Other arguments" + arguments: + - type: "boolean_true" + name: "--skip_copycomplete_check" + description: "Disable the check for the presence of a \"CopyComplete.txt\" file\ + \ in input\ndirectory in case of Illumina data.\n" + info: null + direction: "input" resources: - type: "nextflow_script" path: "main.nf" @@ -187,9 +195,9 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.1" - git_commit: "8da2bf20c5727df1fcdcc997ae87caf562ac4983" - git_remote: "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-15-g8da2bf2" + git_commit: "dd1f93487f4e908999504e1fcdf97f6c59f743d9" + git_remote: "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-16-gdd1f934" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index 133e22f..d920dd7 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -3133,6 +3133,17 @@ meta = [ "multiple_sep" : ";" } ] + }, + { + "name" : "Other arguments", + "arguments" : [ + { + "type" : "boolean_true", + "name" : "--skip_copycomplete_check", + "description" : "Disable the check for the presence of a \\"CopyComplete.txt\\" file in input\ndirectory in case of Illumina data.\n", + "direction" : "input" + } + ] } ], "resources" : [ @@ -3265,9 +3276,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.1", - "git_commit" : "8da2bf20c5727df1fcdcc997ae87caf562ac4983", - "git_remote" : "https://x-access-token:ghs_riWLhGdVGIgxpyesdWQZGphUN4Zki11hGJ7q@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-15-g8da2bf2" + "git_commit" : "dd1f93487f4e908999504e1fcdf97f6c59f743d9", + "git_remote" : "https://x-access-token:ghs_NbivUxJIyO1sd735kE5b6eTS6tHmjH0IsDUF@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-16-gdd1f934" }, "package_config" : { "name" : "demultiplex", @@ -3339,6 +3350,7 @@ workflow run_wf { "input": state.input, "run_information": state.run_information, "demultiplexer": state.demultiplexer, + "skip_copycomplete_check": state.skip_copycomplete_check, "output": "fastq", "output_falco": "qc/fastqc", "output_multiqc": "qc/multiqc_report.html", diff --git a/target/nextflow/runner/nextflow_schema.json b/target/nextflow/runner/nextflow_schema.json index 7153e21..a7bb138 100644 --- a/target/nextflow/runner/nextflow_schema.json +++ b/target/nextflow/runner/nextflow_schema.json @@ -109,6 +109,27 @@ } +} +}, + + + "other arguments" : { + "title": "Other arguments", + "type": "object", + "description": "No description", + "properties": { + + + "skip_copycomplete_check": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete", + "help_text": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete.txt\" file in input\ndirectory in case of Illumina data.\n" + , + "default":false + } + + } }, @@ -157,6 +178,10 @@ "$ref": "#/definitions/output arguments" }, + { + "$ref": "#/definitions/other arguments" + }, + { "$ref": "#/definitions/nextflow input-output arguments" }